GALGO 1.0.11 – Multivariate Variable Selection

GALGO 1.0.11

:: DESCRIPTION

GALGO , an R package based on a genetic algorithm variable selection strategy, primarily designed to develop statistical models from large-scale datasets.

::DEVELOPER

Integrative Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • R

:: DOWNLOAD

 GALGO

:: MORE INFORMATION

Citation

GALGO: an R package for multivariate variable selection using genetic algorithms.
Trevino V, Falciani F.
Bioinformatics. 2006 May 1;22(9):1154-6.

CAIC v.2.6.9 / MacroCAIC – Calculates Phylogenetically Independent Contrasts in one or more Variables

CAIC v.2.6.9 / MacroCAIC

:: DESCRIPTION

CAIC is a freeware comparative analysis package to find and calculates phylogenetically independent contrasts in one or more variables enabling you to test hypotheses of correlated evolution.

MacroCAIC is a software for macroevolutionary trends via comparative analysis. MacroCAIC performs a specialised subset of this analysis, looking at correlates of species richness. From user supplied phylogenies and datasets (describing traits values for members of the phylogeny) MacroCAIC can calculate correlates of species richness, i.e. which traits are associated with abnormal speciation. The phylogeny is used to make these correlations independent, to divorce them from the confounding effects of descent. Traits may be continuous or discrete, and not every trait value need be known for every clade in the phylogeny. Phylogenies may be species level or higher (e.g. genus), dated or undated (i.e. with or without branch-lengths).

::DEVELOPER

Purvis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Macintosh / R package

:: DOWNLOAD

 CAIC / MacroCAIC / CAIC for R

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1995 Jun;11(3):247-51.
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data.
Purvis A, Rambaut A.

Agapow, P.-M. and N.J.B. Isaac. (2002)
MacroCAIC : revealing correlates of species richness by comparative analysis.
Diversity and Distributions 8:41-43.

TOROCOR 1.0 – Assess the Association between Spatially Autocorrelated Variables using Torus-translation tests

TOROCOR 1.0

:: DESCRIPTION

TOROCOR is designed (1) to characterise the spatial autocorrelation of quantitative and/or qualitative variables and (2) to test the significance of the association between variables, notably using torus-translation randomisations. The latter procedure removes the bias of classical tests applied on spatially autocorrelated variables where samples cannot be considered as independent (classical tests tend to be liberal, i.e. rejecting too often the null hypothesis that there is no association between variables).

::DEVELOPER

Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TOROCOR

:: MORE INFORMATION

staRank 0.99.3 – Ranking Variables based on their Stability

staRank 0.99.3

:: DESCRIPTION

staRank is an R package for ranking variables based on their stability.Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  staRank

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 17. [Epub ahead of print]
Stability of gene rankings from RNAi screens.
Siebourg J, Merdes G, Misselwitz B, Hardt WD, Beerenwinkel N.